Details

The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 1000 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc.). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.

BAOSearch is a web-based application for querying, browsing and downloading small molecule biological screening results, including high-throughput screening (HTS) data.BAOSearch content was curated from PubChem by biologists holding Ph.D.s. All assays and their results have been annotated with standardized terms from the BioAssay Ontology (BAO). Leveraging the ontology, BAOSearch has incorporated semantic search capabilities to identify relevant assays.

BioAssay Express allows to explore the similarity of assays within and between organizations. browse and group assays based upon meaningful, detailed criteria like cell type, target, readouts, assay kit, etc., identify similar assays both early on for assay validation and later on for greater confidence in SAR (structure activity relationship). Common Assay Template, which draws from a number of underlying vocabularies created by domain experts, including the BioAssay Ontology (BAO), Drug Target Ontology (DTO), Cell Line Ontology (CLO) and others.

The G protein-coupled receptors (GPCRs) ontology (http://www.bioassayontology.org/bao_gpcr) describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies.

Open PHACTS (Open Pharmacological Concepts Triple Store) is a knowledge management project of the Innovative Medicines Initiative (IMI), a unique partnership between the European Community and the European Federation of Pharmaceutical Industries and Associations (EFPIA).